The Spanish World Cup star – on a 10-game guest loan stint with City – scored 15 minutes after coming on as a second-half substitute, cancelling out Corey Gameiro’s stunning opener early in the second half.
Sydney almost won it at the death with only the crossbar denying Terry Antonis from becoming the hero with a powerful dipping volley.
Much of the pre-match talk had surrounded Melbourne's bow in the league and their stellar-name players.
But it was Gameiro who looked to have stolen the headlines as he curled a superb first-time effort home from 25 yards.
However, Villa showed his class just pass the hour, latching on to Damien Duff's deep cut-back and calmly finding the net from the edge of the penalty area.
City will head home to host Newcastle Jets next week confident thanks to the quality of their maiden showing while Sydney will look to show more in front of their home fans with the visit of fierce local rivals Western Sydney Wanderers.
Elsewhere, a stoppage-time goal from Mitchell Duke helped the Central Coast Mariners snatch a 1-0 victory over the Newcastle Jets in an entertaining F3 Derby at Central Coast Stadium.
The Jets dominated the opening 25 minutes and were highly competitive throughout but Duke's opportunistic score three minutes into injury time denied the visitors what would have been a well-deserved point
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